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Pseudomonas

ABSTRACT: A new species of Pseudomonas putida group

PROVIDER: PRJDB8113 | ENA |

REPOSITORIES: ENA

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			Action	DRS
		Other
	DRR173014_1.fastq.gz	Fastqsanger.gz
	DRR173014_2.fastq.gz	Fastqsanger.gz
	DRR173015_1.fastq.gz	Fastqsanger.gz
	DRR173015_2.fastq.gz	Fastqsanger.gz

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Pseudomonas

Project description:New species of Pseudomonas putida group

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Characterization of DkaiC mutants of Pseudomonas putida KT2440/2 and Pseudomonas protegens CHA0

Project description:KaiC is the central cog of the circadian clock in Cyanobacteria. Close homologs of this protein are widespread among bacteria not known to have a circadian physiology. The function, interaction network, and mechanism of action of these KaiC homologs are still largely unknown. Here, we focus on KaiC homologs found in environmental Pseudomonas species. We characterize experimentally the only KaiC homolog present in Pseudomonas putida KT2440 and Pseudomonas protegens CHA0. Through phenotypic assays and transcriptomics, we show that KaiC is involved in osmotic and oxidative stress resistance in P. putida and in biofilm production in both P. putida and P. protegens.

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Pseudomonas

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Project description:ErfA is a transcription factor of Pseudomonas aeruginosa. We here define the genome-wide binding sites of ErfA by DAP-seq in Pseudomonas aeruginosa PAO1 and IHMA87, Pseudomonas chlororaphis PA23, Pseudomonas protegens CHA0 and Pseudomonas putida KT2440.

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Project description:Transcriptome of the wildtype or evolved Pseudomonas putida KT2440

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Determination of carbon metabolism response regulators regulons in several Pseudomonas species by DAP-seq

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3CB-induced gene expression of Pseudomonas putida KT2440/pSL1 in soil (with RNA amplification)

Project description:Genome-wide scanning of gene expression by microarray techniques was successfully performed on RNA extracted from a sterilized soil inoculated with Pseudomonas putida KT2440/pSL1, which contains a chloroaromatic degrading plasmid, in the presence or absence of 3-chlorobenzoic acid (3CB). The genes showing significant changes in their expression in both triplicate microarray analyses using amplified RNA and single microarray analysis using unamplified RNA were investigated. Pathway analysis revealed that the benzoate degradation pathway underwent the most significant changes following treatment with 3CB. Analysis based on categorization of differentially expressed genes against 3CB revealed new findings about the cellular responses of the bacteria to 3CB, including upregulation of the genes specifically involved in transport of 3CB, and induction of a K+/H+ antiporter complex, an universal stress protein, two cytochrome P450 proteins and an efflux transporter. Downregulated expression of some genes involved in carbon metabolism and the genes belong to a prophage in the presence of 3CB was observed. This study demonstrated the applicability of the method of soil RNA extraction for microarray analysis through a proof-of-concept experiment using a sterilized soil inoculated with Pseudomonas putida KT2440/pSL1. A study using total RNA extracted from soil cultures of Pseudomonas putida KT2440/pSL1. Each chip measures the expression level of 5,341 genes from the Pseudomonas putida KT2440 genome with two sets of six 60-mer probes per gene.

2011-03-29 | E-GEOD-28215 | biostudies-arrayexpress

Pseudomonas putida

Project description:Diversity of Carbapenemases in Pseudomonas putida group species from Brazilian Hospitals

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Project description:Transcription profiling of Pseudomonas putida PP3546 mutant

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Transcriptome analysis of rice roots in response to plant growth promoting rhizobacterium Pseudomonas putida RF3

Project description:To gain an insight into molecular mechanisms underlying plant-microbe interactions gene expression changes in rice plants in response to a plant growth promoting rhizobacteria such as the Pseudomonas putida, root transcriptome analysis through microarray technology was performed from rice roots in response to P. putida RF3. Species of Pseudomonas are well known as biocontrol agents hence defense response and genes related to root exudation of phytochemicals were analysed in detail. For treatment of rice plants with P. putida, aseptically germinated rice seedlings from half strength MS medium were transferred to flasks containing Hoaglands’ nutrient solution, treated with P. putida and incubated for 48 hours in growth chamber in an orbital shaker. Gene expression changes in rice roots were then analyzed by microarray experiment. Untreated roots served as control. Data analysis revealed defense responsive genes to be upregulated with greater fold changes. In addition to defense response genes, few genes involved in secondary metabolism were also upregulated significantly. Validation of microarray data was performed using real time PCR for defense responsive genes (OsPBZ, OsPR101a, OsCHIA, etc). Detailed analysis of the differentially expressed genes reveal the role of P. putida RF3 in inducing systemic resistance in plants thereby immunizing the rice plants against future attacks by pests/pathogens. Our study enhances the current understanding on gene expression changes occurring during plant-microbe associations and thus demonstrates the potential of P. putida RF3 as a biocontrol agent.

2017-12-01 | GSE99881 | GEO

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